The error message is not printed by the Perl script. Most likely, you are using system or backticks (qx) to run an external program. That program is not found by your shell and thus, your shell prints The system cannot find the file specified. The most likely cause is that you have spaces in the path to the program you are invoking, and are not properly quoting the path/name of the program you're invoking.

Usually, checking the return value of system or using autodie would stop your script when it encounters the problem.